Support Python 3.11 on conda?

[schorlton]

Not sure where this issue is arising, but it seems like the pyfastx on conda is not compatible with Python 3.11. I'm under the understanding that it should be?

docker run --rm -it mambaorg/micromamba bash -c "micromamba install pyfastx -c conda-forge -c bioconda -c defaults"
                                                  
                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

bioconda/linux-64                                    4.6MB @   3.7MB/s  1.3s
pkgs/main/linux-64                                   5.5MB @   4.3MB/s  1.3s
pkgs/main/noarch                                   821.1kB @ 550.5kB/s  0.2s
bioconda/noarch                                      4.2MB @   2.5MB/s  1.7s
pkgs/r/noarch                                        1.3MB @ 712.2kB/s  0.6s
pkgs/r/linux-64                                      1.4MB @ 766.0kB/s  0.4s
conda-forge/noarch                                  11.8MB @   3.6MB/s  3.3s
conda-forge/linux-64                                30.7MB @   3.5MB/s  8.9s

Transaction

  Prefix: /opt/conda

  Updating specs:

   - pyfastx


  Package               Version  Build               Channel                   Size
─────────────────────────────────────────────────────────────────────────────────────
  Install:
─────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex           0.1  conda_forge         conda-forge/linux-64       3kB
  + _openmp_mutex           4.5  2_gnu               conda-forge/linux-64      24kB
  + bzip2                 1.0.8  h7f98852_4          conda-forge/linux-64     496kB
  + ca-certificates   2022.12.7  ha878542_0          conda-forge/linux-64     146kB
  + ld_impl_linux-64       2.40  h41732ed_0          conda-forge/linux-64     705kB
  + libffi                3.4.2  h7f98852_5          conda-forge/linux-64      58kB
  + libgcc-ng            12.2.0  h65d4601_19         conda-forge/linux-64     954kB
  + libgomp              12.2.0  h65d4601_19         conda-forge/linux-64     466kB
  + libnsl                2.0.0  h7f98852_0          conda-forge/linux-64      31kB
  + libsqlite            3.40.0  h753d276_0          conda-forge/linux-64     810kB
  + libuuid              2.38.1  h0b41bf4_0          conda-forge/linux-64      34kB
  + libzlib              1.2.13  h166bdaf_4          conda-forge/linux-64      66kB
  + ncurses                 6.3  h27087fc_1          conda-forge/linux-64       1MB
  + openssl               3.1.0  h0b41bf4_0          conda-forge/linux-64       3MB
  + pip                  23.0.1  pyhd8ed1ab_0        conda-forge/noarch         1MB
  + pyfastx               1.0.1  py310h8472f5a_0     bioconda/linux-64         80kB
  + python              3.10.10  he550d4f_0_cpython  conda-forge/linux-64      26MB
  + python_abi             3.10  3_cp310             conda-forge/linux-64       6kB
  + readline                8.2  h8228510_1          conda-forge/linux-64     281kB
  + setuptools           67.6.1  pyhd8ed1ab_0        conda-forge/noarch       580kB
  + tk                   8.6.12  h27826a3_0          conda-forge/linux-64       3MB
  + tzdata                2023c  h71feb2d_0          conda-forge/noarch       118kB
  + wheel                0.40.0  pyhd8ed1ab_0        conda-forge/noarch        56kB
  + xz                    5.2.6  h166bdaf_0          conda-forge/linux-64     418kB
  + zlib                 1.2.13  h166bdaf_4          conda-forge/linux-64      94kB

  Summary:

  Install: 25 packages

  Total download: 40MB

─────────────────────────────────────────────────────────────────────────────────────


Confirm changes: [Y/n] 

Trying with specifying Python 3.11:

docker run --rm -it mambaorg/micromamba bash -c "micromamba install pyfastx python=3.11 -c conda-forge -c bioconda -c defaults" 

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

bioconda/noarch                                      4.2MB @   3.8MB/s  1.1s
bioconda/linux-64                                    4.6MB @   3.8MB/s  1.2s
pkgs/main/linux-64                                   5.5MB @   4.4MB/s  1.3s
pkgs/main/noarch                                   821.1kB @ 564.9kB/s  0.2s
pkgs/r/noarch                                        1.3MB @ 870.7kB/s  0.4s
pkgs/r/linux-64                                      1.4MB @ 846.5kB/s  0.5s
conda-forge/noarch                                  11.8MB @   3.9MB/s  3.1s
conda-forge/linux-64                                30.7MB @   3.7MB/s  8.5s
error    libmamba Could not solve for environment specs
    The following packages are incompatible
    ├─ pyfastx   is installable with the potential options
    │  ├─ pyfastx [0.6.4|0.6.5|0.6.6|0.6.7] would require
    │  │  └─ python >=3.6,<3.7.0a0  with the potential options
    │  │     ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
    │  │     ├─ python 3.6.3 would require
    │  │     │  └─ zlib 1.2.8 , which can be installed;
    │  │     └─ python [3.6.3|3.6.4|3.6.5] would require
    │  │        └─ zlib 1.2.11 , which can be installed;
    │  ├─ pyfastx [0.6.10|0.6.11|...|0.8.4] would require
    │  │  ├─ python >=3.6,<3.7.0a0  with the potential options
    │  │  │  ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
    │  │  │  ├─ python 3.6.3, which can be installed (as previously explained);
    │  │  │  └─ python [3.6.3|3.6.4|3.6.5], which can be installed (as previously explained);
    │  │  └─ python_abi 3.6.* *_cp36m, which can be installed;
    │  ├─ pyfastx [0.6.10|0.6.11|...|1.0.1] would require
    │  │  ├─ python >=3.7,<3.8.0a0 , which can be installed;
    │  │  └─ python_abi 3.7.* *_cp37m, which can be installed;
    │  ├─ pyfastx [0.6.16|0.7.0|...|1.0.1] would require
    │  │  ├─ python >=3.8,<3.9.0a0 , which can be installed;
    │  │  └─ python_abi 3.8.* *_cp38, which can be installed;
    │  ├─ pyfastx [0.6.4|0.6.5|0.6.6|0.6.7] would require
    │  │  └─ python >=3.7,<3.8.0a0 , which can be installed;
    │  ├─ pyfastx [0.8.2|0.8.3|0.8.4|0.9.1|1.0.1] would require
    │  │  ├─ python >=3.9,<3.10.0a0 , which can be installed;
    │  │  └─ python_abi 3.9.* *_cp39, which can be installed;
    │  ├─ pyfastx [0.8.4|0.9.1|1.0.1] would require
    │  │  ├─ python >=3.10,<3.11.0a0 , which can be installed;
    │  │  └─ python_abi 3.10.* *_cp310, which can be installed;
    │  └─ pyfastx [0.9.1|1.0.1] would require
    │     ├─ libzlib >=1.2.13,<1.3.0a0 , which requires
    │     │  └─ zlib 1.2.13 *_4, which conflicts with any installable versions previously reported;
    │     ├─ python >=3.6,<3.7.0a0  with the potential options
    │     │  ├─ python [3.6.0|3.6.1|...|3.6.9], which can be installed;
    │     │  ├─ python 3.6.3, which can be installed (as previously explained);
    │     │  └─ python [3.6.3|3.6.4|3.6.5], which can be installed (as previously explained);
    │     └─ python_abi 3.6.* *_cp36m, which can be installed;
    └─ python 3.11**  is uninstallable because there are no viable options
       ├─ python [3.11.0|3.11.2] conflicts with any installable versions previously reported;
       └─ python [3.11.0|3.11.1|3.11.2] would require
          └─ python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported.
critical libmamba Could not solve for environment specs

Thanks for your help!

[lmdu]

I am sorry. I have not used conda. Currently, I could not fix it.

[shenker]

It's a bioconda-wide issue, see bioconda/bioconda-recipes#37805 and bioconda/bioconda-utils#878.

[schorlton]

Thanks for pointing that out. I'll close this issue and wait for bioconda, which will hopefully be soon given that Python 3.12 was released today.